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Ren S, Zhang L, Tang X, Fan C, Zhao Y, Cheng Q, Zhang Y. Plant Secondary Compounds Promote White Adipose Tissue Browning via Modulation of the Gut Microbiota in Small Mammals. Int J Mol Sci 2023; 24:17420. [PMID: 38139249 PMCID: PMC10743627 DOI: 10.3390/ijms242417420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The browning of white adipose tissue (WAT) is a promising area of research for treating metabolic disorders and obesity in the future. However, studies on plant secondary compounds promoting WAT browning are limited. Herein, we explored the effects of swainsonine (SW) on gut microbiota and WAT browning in captive pikas. SW inhibited body mass gain, increased brown adipose tissue (BAT) mass, and induced WAT browning in pikas. The 16S rDNA sequencing revealed a significant reduction in the alpha diversity and altered community structure of the gut microbiota in captive pikas. However, the addition of SW to the diet significantly increased the alpha diversity of gut microbiota and the relative abundance of Akkermansia, Prevotella, and unclassified_f__Lachnospiraceae, along with the complexity of the microbial co-occurrence network structure, which decreased in the guts of captive pikas. Functional profiles showed that SW significantly decreased the relative abundances of energy metabolism, lipid metabolism, and glycan biosynthesis and metabolism, which were enriched in captive pikas. Furthermore, SW decreased deterministic processes of gut microbiota assembly in July and increased them in November. Finally, the genera Prevotella and unclassified_f__Prevotellaceae were positively correlated with BAT mass. Our results highlighted that plant secondary compounds promote WAT browning by modulating the gut microbiota in small mammals.
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Affiliation(s)
- Shien Ren
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangzhi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Xianjiang Tang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Chao Fan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Yaqi Zhao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Qi Cheng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
| | - Yanming Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810008, China
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2
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Zhen S, Abdul Rauf Z, Fenfen X, Zhan K, Ruiyu M, Wang Z. Microbial fermentation technology for degradation of saponins from peony seed meal. Prep Biochem Biotechnol 2023; 53:1263-1275. [PMID: 36927259 DOI: 10.1080/10826068.2023.2188408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Peony seed meal is a very important feed protein raw material with a high potential for development; however, the presence of some anti-nutritional factors, such as saponins, reduces its reusability. This study aimed to establish ideal microbial fermentation conditions for the degradation of saponins in peony seed meal for its subsequent use in poultry feed. First, saponins were extracted via two methods: ethanol extraction and reflux. Then, response surface methodology and orthogonal array testing were used to establish the optimal conditions for the degradation of saponins by (a) liquid fermentation of single bacteria, (b) liquid fermentation of compound bacteria, and (c) solid-state fermentation. The degradation efficiencies were 40.21% (±1.62), 59.82% (±1.54), and 69.31% (±2.95), respectively. The maximum degradation was obtained via solid-state fermentation, and the soluble protein content for this fermentation product was found to be 14% higher than that of unfermented peony seed meal.
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Affiliation(s)
- Sun Zhen
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Zirwa Abdul Rauf
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Xiao Fenfen
- School of Life Science, Anhui Agricultural University, Hefei, China
| | - Kai Zhan
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, The Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ma Ruiyu
- Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, The Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Zaigui Wang
- School of Life Science, Anhui Agricultural University, Hefei, China
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Pham HHT, Kim DH, Nguyen TL. Wide-genome selection of lactic acid bacteria harboring genes that promote the elimination of antinutritional factors. FRONTIERS IN PLANT SCIENCE 2023; 14:1145041. [PMID: 37180381 PMCID: PMC10171302 DOI: 10.3389/fpls.2023.1145041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/16/2023] [Indexed: 05/16/2023]
Abstract
Anti-nutritional factors (ANFs) substances in plant products, such as indigestible non-starchy polysaccharides (α-galactooligosaccharides, α-GOS), phytate, tannins, and alkaloids can impede the absorption of many critical nutrients and cause major physiological disorders. To enhance silage quality and its tolerance threshold for humans as well as other animals, ANFs must be reduced. This study aims to identify and compare the bacterial species/strains that are potential use for industrial fermentation and ANFs reduction. A pan-genome study of 351 bacterial genomes was performed, and binary data was processed to quantify the number of genes involved in the removal of ANFs. Among four pan-genomes analysis, all 37 tested Bacillus subtilis genomes had one phytate degradation gene, while 91 out of 150 Enterobacteriacae genomes harbor at least one genes (maximum three). Although, no gene encoding phytase detected in genomes of Lactobacillus and Pediococcus species, they have genes involving indirectly in metabolism of phytate-derivatives to produce Myo-inositol, an important compound in animal cells physiology. In contrast, genes related to production of lectin, tannase and saponin degrading enzyme did not include in genomes of B. subtilis and Pediococcus species. Our findings suggest a combination of bacterial species and/or unique strains in fermentation, for examples, two Lactobacillus strains (DSM 21115 and ATCC 14869) with B. subtilis SRCM103689, would maximize the efficiency in reducing the ANFs concentration. In conclusion, this study provides insights into bacterial genomes analysis for maximizing nutritional value in plant-based food. Further investigations of gene numbers and repertories correlated to metabolism of different ANFs will help clarifying the efficiency of time consuming and food qualities.
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Affiliation(s)
- Hai-Ha-Thi Pham
- VK Tech Research Center, NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Do-Hyung Kim
- Department of Aquatic Life Medicine, College of Fisheries Sciences, Pukyong National University, Busan, Republic of Korea
| | - Thanh Luan Nguyen
- Department of Science and Technology, HUTECH University, Ho Chi Minh City, Vietnam
- *Correspondence: Thanh Luan Nguyen,
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4
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Cracraft J. The Hoatzin. Curr Biol 2022; 32:R1068-R1069. [DOI: 10.1016/j.cub.2022.08.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Zhang K, Wang X, Gong X, Sui J. Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. Front Microbiol 2022; 13:858592. [PMID: 35794924 PMCID: PMC9251364 DOI: 10.3389/fmicb.2022.858592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.
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West AG, DeLaunay A, Marsh P, Perry EK, Jolly M, Gartrell BD, Pas A, Digby A, Taylor MW. Gut microbiota of the threatened takahē: biogeographic patterns and conservation implications. Anim Microbiome 2022; 4:11. [PMID: 35078539 PMCID: PMC8790836 DOI: 10.1186/s42523-021-00158-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Aotearoa New Zealand takahē (Porphyrio hochstetteri), once thought to be extinct, is a nationally threatened flightless rail under intensive conservation management. While there has been previous research into disease-related microbes in takahē, little is known about the microbes present in the gastrointestinal tract. Given the importance of gut-associated microbes to herbivore nutrition and immunity, knowledge of these communities is likely to be of considerable conservation value. Here we examined the gut microbiotas of 57 takahē at eight separate locations across Aotearoa New Zealand. RESULTS Faecal samples, taken as a proxy for the hindgut bacterial community, were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq. Phylogenetic analysis of > 2200 amplicon sequence variants (ASVs) revealed nine main bacterial phyla (Acidobacteriota, Actinobacteriota, Bacteroidota, Campilobacterota, Firmicutes, Fusobacteriota, Planctomycetota, Proteobacteria, and Verrucomicrobiota) that accounted for the majority of sequence reads. Location was a significant effect (p value < 0.001, 9999 permutations) that accounted for 32% of the observed microbiota variation. One ASV, classified as Lactobacillus aviarius, was present in all samples at an average relative abundance of 17% (SD = 23.20). There was strong evidence (p = 0.002) for a difference in the abundance of the genus Lactobacillus between locations. A common commensal bacterium previously described in takahē, Campylobacter spp., was also detected in most faecal samples. CONCLUSIONS Location plays a pivotal role in the observed variation among takahē gut bacterial communities and is potentially due to factors such as supplemental feeding and medical treatment experienced by birds housed in captivity at one of the eight sampled sites. These data present a first glimpse of the previously unexplored takahē gut microbiota and provide a baseline for future microbiological studies and conservation efforts.
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Affiliation(s)
- Annie G West
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Anne DeLaunay
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Phil Marsh
- Takahē Recovery Programme, Department of Conservation, Lakefront Drive, Te Anau, New Zealand
| | - Elena K Perry
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Megan Jolly
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Brett D Gartrell
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - An Pas
- New Zealand Centre for Conservation Medicine, Auckland Zoo, Auckland, New Zealand
| | - Andrew Digby
- Takahē Recovery Programme, Department of Conservation, Lakefront Drive, Te Anau, New Zealand
| | - Michael W Taylor
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
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Kang WN, Jin L, Ma HY, Li GQ. Integrated Microbiome-Metabolome Analysis Reveals Stage-Dependent Alterations in Bacterial Degradation of Aromatics in Leptinotarsa decemlineata. Front Physiol 2021; 12:739800. [PMID: 34658924 PMCID: PMC8515180 DOI: 10.3389/fphys.2021.739800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
To avoid potential harm during pupation, the Colorado potato beetle Leptinotarsa decemlineata lives in two different habitats throughout its developmental excursion, with the larva and adult settling on potato plants and the pupa in soil. Potato plants and agricultural soil contain a specific subset of aromatics. In the present study, we intended to determine whether the stage-specific bacterial flora plays a role in the catabolism of aromatics in L. decemlineata. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the operational taxonomic units (OTUs) obtained by sequencing of culture-independent 16S rRNA region enriched a group of bacterial genes involved in the elimination of mono- and polycyclic aromatics at the pupal stage compared with those at the larval and adult periods. Consistently, metabolome analysis revealed that dozens of monoaromatics such as styrene, benzoates, and phenols, polycyclic aromatics, for instance, naphthalene and steroids, were more abundant in the pupal sample. Moreover, a total of seven active pathways were uncovered in the pupal specimen. These ways were associated with the biodegradation of benzoate, 4-methoxybenzoate, fluorobenzoates, styrene, vanillin, benzamide, and naphthalene. In addition, the metabolomic profiles and the catabolism abilities were significantly different in the pupae where their bacteria were removed by a mixture of three antibiotics. Therefore, our data suggested the stage-dependent alterations in bacterial breakdown of aromatics in L. decemlineata.
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Affiliation(s)
- Wei-Nan Kang
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hong-Yu Ma
- Public Laboratory Platform, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Qing Li
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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Effects of Essential Oils-Based Supplement and Salmonella Infection on Gene Expression, Blood Parameters, Cecal Microbiome, and Egg Production in Laying Hens. Animals (Basel) 2021; 11:ani11020360. [PMID: 33535430 PMCID: PMC7912222 DOI: 10.3390/ani11020360] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 11/17/2022] Open
Abstract
One of the main roles in poultry resistance to infections caused by Salmonella is attributed to host immunity and intestinal microbiota. We conducted an experiment that involved challenging Lohmann White laying hens with Salmonella Enteritidis (SE), feeding them a diet supplemented with an EOs-based phytobiotic Intebio®. At 1 and 7 days post-inoculation, the expression profiles of eight genes related to immunity, transport of nutrients in the intestine, and metabolism were examined. Cecal microbiome composition and blood biochemical/immunological indices were also explored and egg production traits recorded. As a result, the SE challenge of laying hens and Intebio® administration had either a suppressive or activating effect on the expression level of the studied genes (e.g., IL6 and BPIFB3), the latter echoing mammalian/human tissue-specific expression. There were also effects of the pathogen challenge and phytobiotic intake on the cecal microbiome profiles and blood biochemical/immunological parameters, including those reflecting the activity of the birds' immune systems (e.g., serum bactericidal activity, β-lysine content, and immunoglobulin levels). Significant differences between control and experimental subgroups in egg performance traits (i.e., egg weight/number/mass) were also found. The phytobiotic administration suggested a positive effect on the welfare and productivity of poultry.
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Gunasekaran M, Lalzar M, Sharaby Y, Izhaki I, Halpern M. The effect of toxic pyridine-alkaloid secondary metabolites on the sunbird gut microbiome. NPJ Biofilms Microbiomes 2020; 6:53. [PMID: 33188208 PMCID: PMC7666580 DOI: 10.1038/s41522-020-00161-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/20/2020] [Indexed: 12/24/2022] Open
Abstract
Sunbirds feed on tobacco tree nectar which contains toxic nicotine and anabasine secondary metabolites. Our aim was to understand the effect of nicotine and anabasine on the gut microbiota composition of sunbirds. Sixteen captive sunbirds were randomly assigned to two diets: artificial nectar either with (treatment) or without (control) added nicotine and anabasine. Excreta were collected at 0, 2, 4 and 7 weeks of treatment and samples were processed for bacterial culture and high-throughput amplicon sequencing of the 16S rRNA gene. The gut microbiome diversity of the treated and control birds changed differently along the seven-week experiment. While the diversity decreased in the control group along the first three samplings (0, 2 and 4 weeks), it increased in the treatment group. The microbiota composition analyses demonstrated that a diet with nicotine and anabasine, significantly changed the birds' gut microbiota composition compared to the control birds. The abundance of nicotine- and anabasine- degrading bacteria in the excreta of the treated birds, was significantly higher after four and seven weeks compared to the control group. Furthermore, analysis of culturable isolates, including Lactococcus, showed that sunbirds' gut-associated bacteria were capable of degrading nicotine and anabasine, consistent with their hypothesised role as detoxifying and nutritional symbionts.
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Affiliation(s)
- Mohanraj Gunasekaran
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Maya Lalzar
- Bioinformatics Service Unit, University of Haifa, Mount Carmel, Haifa, Israel
| | - Yehonatan Sharaby
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Ido Izhaki
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel
| | - Malka Halpern
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Mount Carmel, Haifa, Israel.
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, Israel.
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The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation. mSystems 2020; 5:5/2/e00692-19. [PMID: 32184361 PMCID: PMC7380582 DOI: 10.1128/msystems.00692-19] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gut microbiome may play an important role in insect-plant interactions mediated by plant secondary metabolites, but the microbial communities and functions of toxic plant feeders are still poorly characterized. In the present study, we provide the first metagenome of gut bacterial communities associated with a specialist weevil feeding on saponin-rich and saponin-low camellia seeds, and the results reveal the correlation between bacterial diversity and plant allelochemicals. We also used cultured microbes to establish their saponin-degradative capacity outside the insect. Our results provide new experimental context to better understand how gut microbial communities are influenced by plant secondary metabolites and how the resistance mechanisms involving microbes have evolved to deal with the chemical defenses of plants. The camellia weevil (CW [Curculio chinensis]) is a notorious host-specific predator of the seeds of Camellia species in China, causing seed losses of up to 60%. The weevil is capable of overcoming host tree chemical defenses, while the mechanisms of how these beetles contend with the toxic compounds are still unknown. Here, we examined the interaction between the gut microbes of CW and camellia seed chemistry and found that beetle-associated bacterial symbionts mediate tea saponin degradation. We demonstrate that the gut microbial community profile of CW was significantly plant associated, and the gut bacterial community associated with CW feeding on Camellia oleifera seeds is enriched with genes involved in tea saponin degradation compared with those feeding on Camellia sinensis and Camellia reticulata seeds. Twenty-seven bacteria from the genera Enterobacter, Serratia, Acinetobacter, and Micrococcus subsisted on tea saponin as a sole source of carbon and nitrogen, and Acinetobacter species are identified as being involved in the degradation of tea saponin. Our results provide the first metagenome of gut bacterial communities associated with a specialist insect pest of Camellia trees, and the results are consistent with a potential microbial contribution to the detoxification of tree-defensive chemicals. IMPORTANCE The gut microbiome may play an important role in insect-plant interactions mediated by plant secondary metabolites, but the microbial communities and functions of toxic plant feeders are still poorly characterized. In the present study, we provide the first metagenome of gut bacterial communities associated with a specialist weevil feeding on saponin-rich and saponin-low camellia seeds, and the results reveal the correlation between bacterial diversity and plant allelochemicals. We also used cultured microbes to establish their saponin-degradative capacity outside the insect. Our results provide new experimental context to better understand how gut microbial communities are influenced by plant secondary metabolites and how the resistance mechanisms involving microbes have evolved to deal with the chemical defenses of plants.
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12
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Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JC, Johnson TJ, Knights D. Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). Am J Primatol 2019; 81:e22977. [PMID: 30997937 PMCID: PMC6800578 DOI: 10.1002/ajp.22977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 12/12/2022]
Abstract
The mammalian order primates contains wide species diversity. Members of the subfamily Colobinae are unique amongst extant primates in that their gastrointestinal systems more closely resemble those of ruminants than other members of the primate order. In the growing literature surrounding nonhuman primate microbiomes, analysis of microbial communities has been limited to the hindgut, since few studies have captured data on other gut sites, including the foregut of colobine primates. In this study, we used the red-shanked douc (Pygathrix nemaeus) as a model for colobine primates to study the relationship between gastrointestinal bacterial community structure and gut site within and between subjects. We analyzed fecal and pregastric stomach content samples, representative of the hindgut and foregut respectively, using 16S recombinant DNA (rDNA) sequencing and identified microbiota using closed-reference operational taxonomic unit (OTU) picking against the GreenGenes database. Our results show divergent bacterial communities clearly distinguish the foregut and hindgut microbiomes. We found higher bacterial biodiversity and a higher Firmicutes:Bacteroides ratio in the hindgut as opposed to the foregut. These gut sites showed strong associations with bacterial function. Specifically, energy metabolism was upregulated in the hindgut, whereas detoxification was increased in the foregut. Our results suggest a red-shanked douc's foregut microbiome is no more concordant with its own hindgut than it is with any other red-shanked douc's hindgut microbiome, thus reinforcing the notion that the bacterial communities of the foregut and hindgut are distinctly unique. OPEN PRACTICES: This article has been awarded Open Materials and Open Data badges. All materials and data are publicly accessible via the IRIS Repository at https://www.iris-database.org/iris/app/home/detail?id=york:934328. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Jonathan B. Clayton
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN 55455, USA
- GreenViet Biodiversity Conservation Center, K39/21 Thanh Vinh Street, Son Tra District, Danang, Vietnam
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Robin R. Shields-Cutler
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Department of Biology, Macalester College, 1600 Grand Ave, St. Paul, MN 55105, USA
| | - Susan L. Hoops
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Gabriel A. Al-Ghalith
- Bioinformatics and Computational Biology, 200 Union St SE, University of Minnesota, Minneapolis, MN 55455, USA
| | - John C.M. Sha
- School of Sociology and Anthropology, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Timothy J. Johnson
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 1971 Commonwealth Avenue, Saint Paul, MN 55108, USA
- University of Minnesota, Mid-Central Research and Outreach Center, Willmar, Minnesota, USA
| | - Dan Knights
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN 55455, USA
- Primate Microbiome Project, 6-124 MCB, 420 Washington Ave SE, Minneapolis, MN 55455, USA
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
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13
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Kohl KD, Oakeson KF, Orr TJ, Miller AW, Forbey JS, Phillips CD, Dale C, Weiss RB, Dearing MD. Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.). FEMS Microbiol Ecol 2019; 94:5092587. [PMID: 30202961 DOI: 10.1093/femsec/fiy184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022] Open
Abstract
Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA.,Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Kelly F Oakeson
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Teri J Orr
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Aaron W Miller
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.,Departments of Urology and Immunology, Cleveland Clinic Foundation, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jennifer Sorensen Forbey
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID, 83725 USA
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, TX, 79409, USA
| | - Colin Dale
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT, 84112, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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14
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Qian B, Yin L, Yao X, Zhong Y, Gui J, Lu F, Zhang F, Zhang J. Effects of fermentation on the hemolytic activity and degradation of Camellia oleifera saponins by Lactobacillus crustorum and Bacillus subtilis. FEMS Microbiol Lett 2018; 365:4880443. [DOI: 10.1093/femsle/fny014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/19/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Bingjun Qian
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Jiangsu Vocational College of Medicine, Yancheng, Jiangsu 224005, China
| | - Lirong Yin
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaomin Yao
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaoguang Zhong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Juan Gui
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feifeng Lu
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fuming Zhang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jianhua Zhang
- School of Agriculture and Biology, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai 200240, China
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15
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Itoh H, Tago K, Hayatsu M, Kikuchi Y. Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects. Nat Prod Rep 2018; 35:434-454. [DOI: 10.1039/c7np00051k] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Symbiotic microorganisms degrade natural and artificial toxic compounds, and confer toxin resistance on insect hosts.
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Affiliation(s)
- Hideomi Itoh
- Bioproduction Research Institute
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
- Sapporo 062-8517
- Japan
| | - Kanako Tago
- Institute for Agro-Environmental Sciences
- National Agriculture and Food Research Organization (NARO)
- Tsukuba 305-8604
- Japan
| | - Masahito Hayatsu
- Institute for Agro-Environmental Sciences
- National Agriculture and Food Research Organization (NARO)
- Tsukuba 305-8604
- Japan
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute
- National Institute of Advanced Industrial Science and Technology (AIST) Hokkaido
- Sapporo 062-8517
- Japan
- Graduate School of Agriculture
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16
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Kohl KD, Carey HV. A place for host-microbe symbiosis in the comparative physiologist's toolbox. ACTA ACUST UNITED AC 2017; 219:3496-3504. [PMID: 27852759 DOI: 10.1242/jeb.136325] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
Although scientists have long appreciated that metazoans evolved in a microbial world, we are just beginning to appreciate the profound impact that host-associated microbes have on diverse aspects of animal biology. The enormous growth in our understanding of host-microbe symbioses is rapidly expanding the study of animal physiology, both technically and conceptually. Microbes associate functionally with various body surfaces of their hosts, although most reside in the gastrointestinal tract. Gut microbes convert dietary and host-derived substrates to metabolites such as short-chain fatty acids, thereby providing energy and nutrients to the host. Bacterial metabolites incorporated into the host metabolome can activate receptors on a variety of cell types and, in doing so, alter host physiology (including metabolism, organ function, biological rhythms, neural activity and behavior). Given that host-microbe interactions affect diverse aspects of host physiology, it is likely that they influence animal ecology and, if they confer fitness benefits, the evolutionary trajectory of a species. Multiple variables - including sampling regime, environmental parameters, host metadata and analytical methods - can influence experimental outcomes in host-microbiome studies, making careful experimental design and execution crucial to ensure reproducible and informative studies in the laboratory and field. Integration of microbiomes into comparative physiology and ecophysiological investigations can reveal the potential impacts of the microbiota on physiological responses to changing environments, and is likely to bring valuable insights to the study of host-microbiome interactions among a broad range of metazoans, including humans.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 53705, USA
| | - Hannah V Carey
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
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17
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Hammer TJ, Bowers MD. Gut microbes may facilitate insect herbivory of chemically defended plants. Oecologia 2015; 179:1-14. [DOI: 10.1007/s00442-015-3327-1] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/16/2015] [Indexed: 12/17/2022]
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18
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Godoy-Vitorino F, Leal SJ, Díaz WA, Rosales J, Goldfarb KC, García-Amado MA, Michelangeli F, Brodie EL, Domínguez-Bello MG. Differences in crop bacterial community structure between hoatzins from different geographical locations. Res Microbiol 2012; 163:211-20. [PMID: 22313738 DOI: 10.1016/j.resmic.2012.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 12/30/2011] [Indexed: 11/30/2022]
Abstract
The hoatzin is the only known folivorous bird with foregut fermentation, and is distributed in Venezuela in rivers of the central savannas to the eastern Orinoco River. Differences in diet are expected to affect the digestive microbiota and we hypothesized that hoatzins from different habitats might have a different crop microbiota. We thus characterized the microbiota of six birds from the Cojedes and Orinoco Rivers using the G2 PhyloChip and, in parallel, we compared plant availability and foraging behavior of the hoatzins from the two locations. Plant composition differed between the 2 locations, which shared 5 out of 18 plant families and 1 plant genus--Coccoloba--that was highly consumed in both locations. The PhyloChip detected ∼1600 phylotypes from 42 phyla. There was a core microbiota with ~50% of the OTUs shared by at least 4 of the 6 individuals, but there were also differences in the crop microbiota of animals from the two regions. There existed a higher relative abundance of Alphaproteobacteria and Actinobacteria in the crops of birds from the Cojedes River and of Clostridia and Deltaproteobacteria in the crops of birds from the Orinoco River. The results showed both a core crop microbiota and also the bacterial taxa responsible for geographical differences among individuals from the two locations with different vegetation, suggesting an effect of both diet and geography in shaping the crop bacterial community of the hoatzin.
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Affiliation(s)
- Filipa Godoy-Vitorino
- Department of Biology, University of Puerto Rico, P.O. Box 23360, San Juan, PR 00931
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19
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Kohl KD. Diversity and function of the avian gut microbiota. J Comp Physiol B 2012; 182:591-602. [PMID: 22246239 DOI: 10.1007/s00360-012-0645-z] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2011] [Revised: 12/30/2011] [Accepted: 01/04/2012] [Indexed: 01/16/2023]
Abstract
The intestinal microbiota have now been shown to largely affect host health through various functional roles in terms of nutrition, immunity, and other physiological systems. However, the majority of these studies have been carried out in mammalian hosts, which differ in their physiological traits from other taxa. For example, birds possess several unique life history traits, such as hatching from eggs, which may alter the interactions with and transmission of intestinal microbes compared to most mammals. This review covers the diversity of microbial taxa hosted by birds. It also discusses how avian microbial communities strongly influence nutrition, immune function, and processing of toxins in avian hosts, in manners similar to and different from mammalian systems. Finally, areas demanding further research are identified, along with descriptions of existing techniques that could be employed to answer these questions.
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Affiliation(s)
- Kevin D Kohl
- Department of Biology, University of Utah, 257 S. 1400 East, Salt Lake City, UT, 84112, USA.
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20
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Wright ADG, Northwood KS, Obispo NE. Rumen-like methanogens identified from the crop of the folivorous South American bird, the hoatzin (Opisthocomus hoazin). ISME JOURNAL 2009; 3:1120-6. [DOI: 10.1038/ismej.2009.41] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Bacterial community in the crop of the hoatzin, a neotropical folivorous flying bird. Appl Environ Microbiol 2008; 74:5905-12. [PMID: 18689523 DOI: 10.1128/aem.00574-08] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hoatzin is unique among known avian species because of the fermentative function of its enlarged crop. A small-bodied flying foregut fermenter is a paradox, and this bird provides an interesting model to examine how diet selection and the gut microbiota contribute to maximizing digestive efficiency. Therefore, we characterized the bacterial population in the crop of six adult hoatzins captured from the wild. A total of 1,235 16S rRNA gene sequences were grouped into 580 phylotypes (67% of the pooled species richness sampled, based on Good's coverage estimator, with C(ACE) and Chao1 estimates of 1,709 and 1,795 species-level [99% identity] operational taxonomic units, respectively). Members of 9 of the approximately 75 known phyla in Bacteria were identified in this gut habitat; the Firmicutes were dominant (67% of sequences, belonging to the classes Clostridia, Mollicutes, and Bacilli), followed by the Bacteroidetes (30%, mostly in the order Bacteroidales), Proteobacteria (1.8%), and Lentisphaerae, Verrucomicrobia, TM7, Spirochaetes, Actinobacteria, and Aminanaerobia (all <0.1%). The novelty in this ecosystem is great; 94% of the phylotypes were unclassified at the "species" level and thus likely include novel cellulolytic lineages.
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